T-Trees

A novel tree-based approach for Genome-Wide Association Studies

Supplementary data

Back

---

---

1	Best: rs7539166 (4)	Gene	15.21-15.24Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4661579	C1orf126 NCBI Gene Pubmed Genecard	15210793	0.05056	1	0.8534	0.1234	0.0006	99
	rs10754883	C1orf126 NCBI Gene Pubmed Genecard	15216479	0.05105	0.4322	0.274	0.1399	0.00071	91
	rs4661581	TMEM51 NCBI Gene Pubmed Genecard	15227360	0.0548	0.1232	0.8674	0.01435	0.0011	72
	rs7539166	TMEM51 NCBI Gene Pubmed Genecard	15241211	0.06697	2.265e-243	0.006298	2.392e-14	0.021	9
1	Best: rs6679677 (2)	Gene	113.89-114.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1230666	MAGI3 NCBI Gene Pubmed Genecard	113885452	0.1694	0.1058	0.4527	2.343e-16	0.00011	163
	rs6679677		114015850	0.1239	0.01234	0.241	1.123e-24	0.00082	80
2	Best: rs13425033 (3)	Gene	105.54-105.55Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs13425033		105535143	0.06852	8.863e-264	0.002604	1.403e-25	0.024	7
	rs6708103		105538696	0.05544	7.469e-07	2.138e-05	0.8184	0.00023	131
	rs6725019		105545462	0.06407	0.4094	0.1781	0.2659	0.00012	157
2	Best: rs1440065 (7)	Gene	223.66-223.73Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6712467		223659012	0.05671	1	1	0.415	0.00077	85
	rs6743849		223666584	0.05748	1	0.8609	0.4442	0.00074	86
	rs1440065		223675115	0.07224	1.999e-274	0.009171	5.4e-26	0.028	5
	rs1345012		223701268	0.05898	0.001538	5.424e-05	0.5327	0.00012	160
	rs1550425		223711573	0.05674	0.5333	1	0.2958	0.00014	145
	rs7557492		223713606	0.05685	0.213	0.8584	0.2578	0.0002	134
	rs12987851		223725676	0.05545	0.5227	0.4684	0.3133	0.0002	135
3	Best: rs17665418 (3)	Gene	71.93-71.94Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17665418		71931855	0.08384	8.504e-285	1.577e-05	8.541e-21	0.031	2
	rs17721983		71938626	0.07131	0.8543	0.2223	0.3286	0.00093	77
	rs17665544		71941680	0.06246	0.5263	0.3463	0.4291	0.00047	105
4	Best: rs1553460 (3)	Gene	17.85-17.87Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1039539		17850862	0.2562	0.01941	0.3804	0.9229	6.5e-05	195
	rs11938418		17871212	0.2818	0.4894	0.03268	0.675	0.00026	125
	rs1553460		17872130	0.3079	1.279e-104	2.877e-05	1.163e-22	0.0073	23
6	Best: rs4959053 (3)	Gene	31.17-31.22Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4947296		31166157	0.0566	0.205	0.07848	0.683	0.0001	164
	rs4959053	PSORS1C1 NCBI Gene Pubmed Genecard	31207556	0.07439	7.302e-273	0.0003026	1.115e-22	0.027	6
	rs2240066	CCHCR1 NCBI Gene Pubmed Genecard	31222314	0.04339	1	0.4865	0.382	0.00025	127
6	Best: rs6457620 (75)	Gene	31.73-32.79Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs805297	APOM NCBI Gene Pubmed Genecard	31730585	0.3208	0.3754	0.4397	5.337e-23	0.00014	147
	rs707974	C6orf47 NCBI Gene Pubmed Genecard GPANK1 NCBI Gene Pubmed Genecard	31737478	0.1419	0.226	0.04036	1.435e-25	0.00065	95
	rs707939	MSH5 NCBI Gene Pubmed Genecard MSH5-SAPCD1 NCBI Gene Pubmed Genecard	31834667	0.3684	0.4461	0.8308	5.535e-33	0.00039	114
	rs2075800	HSPA1L NCBI Gene Pubmed Genecard	31885925	0.3569	0.7761	0.1109	3.593e-32	0.00043	112
	rs644045		31991936	0.3392	0.1731	0.003932	2.971e-18	0.0001	167
	rs541862	CFB NCBI Gene Pubmed Genecard	32024930	0.07707	1	0.2672	4.834e-13	8.2e-05	176
	rs2072633	CFB NCBI Gene Pubmed Genecard RDBP NCBI Gene Pubmed Genecard	32027557	0.4191	0.3878	0.0006304	4.246e-26	0.00036	119
	rs550513	RDBP NCBI Gene Pubmed Genecard	32028666	0.0785	1	0.3876	1.381e-13	7.1e-05	187
	rs17421624	TNXB NCBI Gene Pubmed Genecard	32174155	0.3482	0.9244	0.1042	3.2e-35	0.00067	93
	rs9296009		32222493	0.2758	0.5749	0.3469	1.285e-37	0.00079	83
	rs3134926		32308125	0.2547	1	0.7539	2.546e-24	0.00071	90
	rs9267954		32321030	0.3245	0.1019	0.08553	6.153e-41	0.00073	88
	rs3115576		32324828	0.4484	0.02601	0.1369	1.382e-20	7.6e-05	182
	rs6936204		32325070	0.3217	0.4727	0.03364	6.018e-23	0.00012	158
	rs9267971		32325163	0.448	0.03262	0.1471	2.861e-20	7.3e-05	184
	rs4959090		32327940	0.1718	0.7308	0.2008	0.07183	7e-05	188
	rs1265777	C6orf10 NCBI Gene Pubmed Genecard	32381136	0.4417	0.02523	0.5588	4.051e-44	0.0011	68
	rs9268230	C6orf10 NCBI Gene Pubmed Genecard	32395545	0.2989	0.0002872	0.05199	2.269e-13	0.00019	138
	rs574710	C6orf10 NCBI Gene Pubmed Genecard	32396168	0.4435	0.01358	0.6133	4.039e-43	0.0012	67
	rs539703	C6orf10 NCBI Gene Pubmed Genecard	32396440	0.4414	0.01361	0.4591	1.677e-43	0.0011	70
	rs3132959	C6orf10 NCBI Gene Pubmed Genecard	32406920	0.2019	0.355	0.05227	2.108e-27	0.00061	98
	rs926591	C6orf10 NCBI Gene Pubmed Genecard	32413668	0.4417	0.01753	0.5591	2.133e-43	0.0011	71
	rs9368716	C6orf10 NCBI Gene Pubmed Genecard	32414068	0.4951	0.04033	0.333	6.553e-26	0.00017	142
	rs4959093	C6orf10 NCBI Gene Pubmed Genecard	32421075	0.4416	0.01753	0.5334	5.006e-43	0.0011	69
	rs910049	C6orf10 NCBI Gene Pubmed Genecard	32423705	0.2059	0.08433	0.0002171	2.559e-27	0.00052	102
	rs2894249	C6orf10 NCBI Gene Pubmed Genecard	32433813	0.198	0.3455	0.4025	1.218e-25	0.00047	106
	rs3129932	C6orf10 NCBI Gene Pubmed Genecard	32444105	0.2016	0.4571	0.05852	1.066e-27	0.00068	92
	rs9268402	C6orf10 NCBI Gene Pubmed Genecard	32449331	0.4374	0.3227	0.9119	6.519e-59	0.0026	39
	rs9268403	C6orf10 NCBI Gene Pubmed Genecard	32449451	0.3665	0.08447	0.4866	1.473e-54	0.0018	48
	rs12201454		32451664	0.3662	0.1025	0.4594	1.41e-54	0.0018	49
	rs9268429		32453030	0.3727	0.008963	0.001964	1.046e-52	0.0015	57
	rs12528797		32453064	0.1244	0.01078	0.5169	7.403e-06	7.9e-05	179
	rs6930777		32459544	0.1237	0.01841	0.3023	2.755e-06	7.7e-05	181
	rs2076533	BTNL2 NCBI Gene Pubmed Genecard	32471505	0.4865	0.9216	0.7651	2.814e-62	0.0026	40
	rs2076530	BTNL2 NCBI Gene Pubmed Genecard	32471794	0.4816	0.9213	0.9406	2.788e-60	0.0025	41
	rs9268480	BTNL2 NCBI Gene Pubmed Genecard	32471822	0.3666	0.1025	0.4598	2.965e-54	0.0018	53
	rs3806156	BTNL2 NCBI Gene Pubmed Genecard	32481676	0.4221	0.2276	0.8744	1.988e-35	0.00071	89
	rs3763307	BTNL2 NCBI Gene Pubmed Genecard	32482600	0.3666	0.09311	0.4339	2.06e-54	0.0018	51
	rs3135377		32493377	0.1903	0.6362	1	1.467e-21	0.00026	126
	rs9268557		32497283	0.45	0.1979	0.8534	2.189e-64	0.0029	37
	rs9268560		32497490	0.4146	0.03803	0.9705	1.347e-66	0.0035	34
	rs3135363		32497626	0.2325	0.8123	0.2203	4.522e-24	0.00024	129
	rs7756262		32506653	0.4205	0.8871	0.6284	3.132e-41	0.00061	97
	rs9268645	HLA-DRA NCBI Gene Pubmed Genecard	32516505	0.43	0.2272	0.752	4.329e-45	0.00098	73
	rs7194	HLA-DRA NCBI Gene Pubmed Genecard	32520458	0.3415	0.5795	0.7004	1.737e-50	0.0019	46
	rs9268853		32537621	0.4261	0.285	0.8735	1.853e-51	0.0018	52
	rs9268856		32537697	0.2174	0.3009	0.6257	1.305e-27	0.00044	111
	rs9268858		32537736	0.4264	0.2269	0.9366	2.007e-51	0.0017	54
	rs9268861		32537872	0.1826	0.6331	0.5022	1.313e-16	7.1e-05	186
	rs9268862		32538145	0.2163	0.1953	0.8826	5.104e-26	0.00032	122
	rs4428528		32538340	0.1912	0.005743	0.0001929	1.688e-21	0.0001	166
	rs7766843		32538707	0.2176	0.2283	0.7698	1.374e-27	0.00051	104
	rs7746922		32538953	0.2254	0.008456	5.227e-05	2.68e-31	0.00041	113
	rs7747521		32539083	0.217	0.2285	0.8068	4.793e-27	0.00045	109
	rs9268877		32539125	0.3555	0.8722	0.2401	1.848e-10	0.00013	151
	rs9268878		32539270	0.2177	0.2642	0.6964	3.315e-27	0.00047	107
	rs9269186	HLA-DRB3 NCBI Gene Pubmed Genecard	32556394	0.2159	0.6041	0.3265	2.847e-27	0.00044	110
	rs7749092		32557028	0.2229	0.2914	0.4137	1.124e-34	0.0014	59
	rs615672	LOC100507709 NCBI Gene Pubmed Genecard LOC100507714 NCBI Gene Pubmed Genecard	32682149	0.2915	0.1126	0.9668	1.964e-28	0.00053	101
	rs9271208		32686981	0.2367	0.2414	0.5042	2.731e-13	0.00013	155
	rs4530903		32689867	0.1214	0.02285	0.8467	2.027e-07	7.9e-05	180
	rs9271850		32703038	0.2732	0.2976	0.0001795	1.709e-43	0.0013	64
	rs3129768		32703061	0.1505	0.1159	0.204	5.881e-21	0.00019	137
	rs9272219		32710247	0.2242	0.3352	0.6979	1.543e-20	0.00036	120
	rs7775228		32766057	0.1056	0.8589	0.06839	1.006e-19	0.00058	100
	rs6457617		32771829	0.4353	0.7883	0.631	2.498e-80	0.0051	27
	rs6457620		32771977	0.4347	0.7467	0.6054	1.102e-80	0.0052	26
	rs2647015		32772071	0.08796	0.8379	0.01072	9.816e-15	0.00037	117
	rs2647046		32776314	0.3448	0.5781	0.2189	1.078e-52	0.0016	56
	rs2858308		32777978	0.08805	1	0.01802	3.493e-14	0.00031	123
	rs9275418		32778222	0.3058	0.1446	0.4041	4.609e-48	0.002	45
	rs9275523		32782972	0.2897	0.2382	0.565	1.276e-57	0.0029	36
	rs9275572		32786977	0.3608	0.8567	0.8799	1.203e-60	0.0027	38
	rs3957146		32789508	0.1507	0.0124	0.2152	1.717e-44	0.0012	65
	rs3916765		32793528	0.1479	0.3248	0.1426	4.572e-19	0.00011	161
7	Best: rs4718582 (7)	Gene	66.40-66.45Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4718581		66397010	0.01596	1	0.03771	0.9332	0.00014	148
	rs4718582		66398211	0.05589	0.02344	0.3988	3.064e-75	0.014	12
	rs4718584		66398998	0.2377	0.9494	0.9592	0.6225	0.00012	156
	rs10950076		66407425	0.3523	0.261	0.6868	0.5246	6e-05	200
	rs6460356		66407883	0.2154	0.5354	0.2311	0.8584	9.7e-05	168
	rs4636085		66418070	0.01723	1	0.1999	0.7477	0.00018	141
	rs7779218		66448664	0.01255	1	1	0.8506	8e-05	177
7	Best: rs7789415 (6)	Gene	157.71-157.73Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2335167	PTPRN2 NCBI Gene Pubmed Genecard	157713424	0.4381	0.7778	0.1886	0.2536	0.00027	124
	rs11765319	PTPRN2 NCBI Gene Pubmed Genecard	157726266	0.4004	0.8474	0.2326	0.5212	0.00079	84
	rs11769149	PTPRN2 NCBI Gene Pubmed Genecard	157726603	0.3988	0.9615	0.3547	0.5633	0.00096	76
	rs7787923	PTPRN2 NCBI Gene Pubmed Genecard	157726788	0.4319	0.4456	0.7042	0.8309	0.00023	130
	rs7789415	PTPRN2 NCBI Gene Pubmed Genecard	157727093	0.04264	1	2.553e-06	2.454e-66	0.013	14
	rs4909222	PTPRN2 NCBI Gene Pubmed Genecard	157727571	0.399	0.9231	0.3748	0.5346	0.00073	87
9	Best: rs16908561 (7)	Gene	24.52-24.61Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16908434		24518128	0.03737	0.4387	0.027	0.0407	0.00012	159
	rs16908449		24520857	0.03755	0.4386	0.008605	0.03157	8.8e-05	173
	rs1329846		24522443	0.03633	1	0.08714	0.05694	8.3e-05	175
	rs16908561		24592765	0.04119	1.219e-159	0.04914	0.0001345	0.0088	21
	rs16908610		24601547	0.03531	0.6913	0.03691	0.05332	0.00013	152
	rs16908647		24607036	0.03394	0.6791	0.5925	0.09287	0.00013	149
	rs7041483		24611394	0.03322	0.4019	0.5882	0.06097	0.00016	144
11	Best: rs10501805 (2)	Gene	93.02-93.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12291408		93020479	0.006784	1	1	0.07362	6.2e-05	198
	rs10501805		93031602	0.03276	0.0001056	1	1.731e-62	0.01	18
12	Best: rs10843660 (4)	Gene	30.25-30.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10743704		30249349	0.2987	0.002786	0.402	0.9452	0.0014	60
	rs10843660		30259724	0.3838	2.236e-75	0.03536	4.346e-30	0.007	25
	rs9669515		30260529	0.2978	0.003327	0.4791	0.8365	0.0014	58
	rs1157480		30264271	0.2996	0.007842	0.3771	0.7829	0.0013	63
15	Best: rs899848 (2)	Gene	27.77-27.85Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs260536		27770398	0.02231	1	1	0.2277	7.4e-05	183
	rs899848	TJP1 NCBI Gene Pubmed Genecard	27848922	0.02736	5.427e-112	0.6325	1.512e-07	0.0036	33
17	Best: rs3785579 (9)	Gene	62.46-62.65Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9892020		62460904	0.153	0.9285	0.0001116	0.9768	0.0071	24
	rs4790993		62465677	0.2983	0.8682	0.4015	0.8546	0.00019	136
	rs2159210		62466422	0.2416	0.7092	0.9593	0.2209	0.0081	22
	rs3785579	CACNG1 NCBI Gene Pubmed Genecard	62472963	0.2705	0	0.02123	0	0.26	1
	rs7217216	HELZ NCBI Gene Pubmed Genecard	62500117	0.2122	0.417	1	0.1438	0.00091	78
	rs10491170	HELZ NCBI Gene Pubmed Genecard	62512481	0.2119	0.3791	1	0.151	0.00086	79
	rs8066806	HELZ NCBI Gene Pubmed Genecard	62629181	0.1657	0.03412	0.6814	0.1341	0.00097	74
	rs8080100	HELZ NCBI Gene Pubmed Genecard	62642504	0.1535	0.6074	0.2431	0.1036	0.0013	61
	rs16960718	HELZ NCBI Gene Pubmed Genecard	62647612	0.1535	0.6684	0.5107	0.08091	0.0012	66
18	Best: rs4799934 (5)	Gene	33.34-33.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-1817219		33339731	0.05415	0.3671	0.4616	0.7091	0.00066	94
	rs1786811	CELF4 NCBI Gene Pubmed Genecard	33340772	0.06088	0.000951	0.2584	0.9301	0.00081	81
	rs1786776	CELF4 NCBI Gene Pubmed Genecard	33341455	0.06386	0.4357	0.352	1	0.0008	82
	rs1786768	CELF4 NCBI Gene Pubmed Genecard	33347744	0.06233	0.3136	1	0.8966	0.00097	75
	rs4799934	CELF4 NCBI Gene Pubmed Genecard	33357665	0.07761	3.882e-286	0.002834	8.281e-27	0.031	3
23	Best: rs6588810 (3)	Gene	1.02-1.80Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5025647		1016564	0.02324	1	0.1666	9.849e-07	6.9e-05	189
	rs6422988		1499735	0.4706	1.206e-100	8.899e-105	1.32e-17	0.00046	108
	rs6588810		1796945	0.01539	2.762e-06	2.22e-05	1.734e-08	0.0019	47
23	Best: rs5934184 (5)	Gene	14.23-14.50Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16979557		14228288	0.2003	0.6047	1	0.02607	7.3e-05	185
	rs6526752	GLRA2 NCBI Gene Pubmed Genecard	14366062	0.294	0.841	0.3016	0.0004227	0.0001	165
	rs5934184	GLRA2 NCBI Gene Pubmed Genecard	14420578	0.2393	0.4445	0.5308	0.001837	0.00011	162
	rs5935795	GLRA2 NCBI Gene Pubmed Genecard	14477078	0.259	0.4738	0.5097	0.009681	6.5e-05	193
	rs10521644	GLRA2 NCBI Gene Pubmed Genecard	14503094	0.2636	0.5712	0.05245	0.004958	7.9e-05	178